[Bio-software] Re: Bio-soft Digest, Vol 32, Issue 2

Amit Dattatreya Parhar via bio-soft%40net.bio.net (by amit.p from ocimumbio.com)
Thu Jan 10 01:06:41 EST 2008


Hello everybody, I need an advice.
>
> I want to align 30 homolog non-coding sequencess of  about 1800bp length
with low similarity. In addition to substitutions and gaps, these sequences
contain short and long tandem repeats in several non-identical locations.
>
> Which software is optimal for such an alignment? is it clustlW? T-coffee?
maybe other software?
> I would like to avoid using repeatmasker if possible so the software has
to ignore the disrupting repeats.
>
> Thanks in advance,
> Giladâ?Z

check out his algorithm might be of help

http://nar.oxfordjournals.org/cgi/content/full/34/20/5932

regards,
Amit Parhar
Ocimum Biosolutions

----- Original Message ----- 
From: <bio-soft-request from oat.bio.indiana.edu>
To: <bio-soft from magpie.bio.indiana.edu>
Sent: Wednesday, January 09, 2008 10:34 PM
Subject: Bio-soft Digest, Vol 32, Issue 2


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> Today's Topics:
>
>    1. Advice about DNA alignment (Gilad Lehmann)
>    2. Re: Advice about DNA alignment (darked)
>    3. Grouping of proteins by function/category (hains from uow.edu.au)
>    4. Re: Grouping of proteins by function/category (darked)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 08 Jan 2008 12:08:37 GMT
> From: Gilad Lehmann <giladle from bgu.ac.il>
> Subject: [Bio-software] Advice about DNA alignment
> To: bio-soft from magpie.bio.indiana.edu
> Message-ID: <fa17db1f1c4e2.478367c5 from bgu.ac.il>
> Content-Type: text/plain; charset=utf-8
>
> Hello everybody, I need an advice.
>
> I want to align 30 homolog non-coding sequencess of  about 1800bp length
with low similarity. In addition to substitutions and gaps, these sequences
contain short and long tandem repeats in several non-identical locations.
>
> Which software is optimal for such an alignment? is it clustlW? T-coffee?
maybe other software?
> I would like to avoid using repeatmasker if possible so the software has
to ignore the disrupting repeats.
>
> Thanks in advance,
> Giladâ?Z
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 8 Jan 2008 11:44:07 -0800 (PST)
> From: darked <darek.kedra from gmail.com>
> Subject: [Bio-software] Re: Advice about DNA alignment
> To: bionet-software from moderators.isc.org
> Message-ID:
> <4d2d3699-50a5-4b47-b8f4-cdcf5ae0edfc from r60g2000hsc.googlegroups.com>
> Content-Type: text/plain; charset=windows-1256
>
> On Jan 8, 12:08 pm, Gilad Lehmann <gila... from bgu.ac.il> wrote:
> > Hello everybody, I need an advice.
> >
> > I want to align 30 homolog non-coding sequencess of  about 1800bp length
with low similarity. In addition to substitutions and gaps, these sequences
contain short and long tandem repeats in several non-identical locations.
> >
> > Which software is optimal for such an alignment? is it clustlW?
T-coffee? maybe other software?
> > I would like to avoid using repeatmasker if possible so the software has
to ignore the disrupting repeats.
> >
> > Thanks in advance,
> > Giladý
>
> Well, if you call them homolog than somehow you selected these
> sequences based on similarity,  I assume. So if you deal with non-
> coding regions close to a gene you may include 'anchors' -> extend
> sequences to include i.e. coding exons.
>
> >Which software is optimal for such an alignment? is it clustlW? T-coffee?
maybe other software?
>  You will need something more advanced me thinks.
>
> Check this paper
http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1431#B15
> and Aubergine:
> http://zeus.cs.vu.nl/programs/aubergenewww/
>
> Easy web-interface: MultiPipMaker
> http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker
>
> Shameless plug:
> http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial#DNA_alignment
>
> Comments about tools accuracy/ease of use etc. will be greatly
> appreciated ;-)
>
> Darek Kedra
> http://openwetware.org/wiki/Wikiomics
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 8 Jan 2008 20:22:29 -0800 (PST)
> From: "hains from uow.edu.au" <hains from uow.edu.au>
> Subject: [Bio-software] Grouping of proteins by function/category
> To: bionet-software from moderators.isc.org
> Message-ID:
> <1c072af6-82fe-4efd-a7be-ac5a0f730b05 from y5g2000hsf.googlegroups.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi all,
>
> I have a rather long list of proteins (about 230) that I want to group
> based on the function of each protein, such as structural,
> cytoplasmic, growth factor, that kind of thing. I'm after general
> groupings for the proteins. Does anyone know of a database that has
> this kind of info that I can submit my AC codes in a batch and have
> the result spat out the other end?
>
> I know there are various databases that will have this kind of info,
> but is there an easier way than looking each protein up individually?
>
> Thanks,
>
> Peter
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 9 Jan 2008 04:30:33 -0800 (PST)
> From: darked <darek.kedra from gmail.com>
> Subject: [Bio-software] Re: Grouping of proteins by function/category
> To: bionet-software from moderators.isc.org
> Message-ID:
> <cce905ce-ab8f-494d-9be7-6a5f60d0d8dc from f47g2000hsd.googlegroups.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Jan 9, 4:22 am, "ha... from uow.edu.au" <ha... from uow.edu.au> wrote:
> > Hi all,
> >
> > I have a rather long list of proteins (about 230) that I want to group
> > based on the function of each protein, such as structural,
> > cytoplasmic, growth factor, that kind of thing. I'm after general
> > groupings for the proteins. Does anyone know of a database that has
> > this kind of info that I can submit my AC codes in a batch and have
> > the result spat out the other end?
> >
> > I know there are various databases that will have this kind of info,
> > but is there an easier way than looking each protein up individually?
> >
> > Thanks,
> >
> > Peter
>
> Hi,
>
> it depends on how fine-grained output you need. As long as you stay
> within gene ontology terms  try G:profiler
> http://biit.cs.ut.ee/gprofiler/
>
> Best,
> Darek Kedra
> http://openwetware.org/wiki/Wikiomics
>
>
>
> ------------------------------
>
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> End of Bio-soft Digest, Vol 32, Issue 2
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